Fig. 4: snRNAseq identifies compositional patterns that correlate with survival.

a Bar plots demonstrating the fractional composition of each one of 16 samples analyzed by snRNAseq (8 primary IDH-WT glioma from 7 patients, one case was divided to core and overlying cortex, and 8 recurrent IDH-WT glioblastoma). The left panel shows the fraction of neoplastic (CNVpos) and non-neoplastic (CNVneg) nuclei. The middle panel shows the fraction of the non-neoplastic nuclei contributed by neurons, oligodendrocytes, OPCs, astrocytes, myeloid cells, endothelial cells, and astrocytes. The right panel shows the fraction of the neoplastic nuclei contributed by proneural/progenitor-like glioma (gl_PN1, gl_PN2), astrocyte-like/mesenchymal glioma (gl_Mes1, gl_Mes2), and proliferative glioma (gl_Pro1, and gl_Pro2). The description of glioma states is provided in the supplementary results. b Principal component analysis of the fractional composition matrix of 19 samples encompassing eight primary and eight recurrent gliomas plus three epilepsy samples (Supplementary dataset 1). The tissue composition matrix consists of the percentage of nuclei per each tissue state. Immune-cell states are: mgTAMs (microglia-derived Tumor-associated macrophages), moTAM (monocyte-derived TAMs), prTAM (proliferative TAM), Myel1 (baseline myeloid cells), and T cells. Astrocyte states include baseline (protoplasmic) astrocytes (Ast1), reactive CD44 + astrocytes (Ast3), and reactive astrocytes with expression of non-astrocyte genes (Ast2)—see text and supplementary results for additional description of these cell states. CNVpos represents the total percentage of all glioma states per sample. Individual glioma states were not used in PCA calculation, rather they were used as supplementary quantitative variables and their coordinates were predicted from the PCA analysis—see methods. c Kaplan–Meier survival plot graphing survival (days) in the combined TCGA and CGGA RNAseq datasets. The samples were classified based on positive or negative enrichment for the PC2 gene signature. Statistical significance was computed using the log-rank test.